Loading report..

Highlight Samples

This report has flat image plots that won't be highlighted.
See the documentation for help.

Regex mode off

    Rename Samples

    This report has flat image plots that won't be renamed.
    See the documentation for help.

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      This report has flat image plots that won't be hidden.
      See the documentation for help.

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.


        Load Settings

        Choose a saved report profile from the dropdown box below:

        About MultiQC

        This report was generated using MultiQC, version 1.6

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2020-02-03, 14:21 based on data in: /hps/research1/birney/users/adrien/analyses/medaka_RNA_illumina/Indigene_pilot/RNA_pipeline2/results


        General Statistics

        Showing 580 samples.

        loading..

        featureCounts

        Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Samtools

        Samtools is a suite of programs for interacting with high-throughput sequencing data.

        Percent Mapped

        Alignment metrics from samtools stats; mapped vs. unmapped reads.

        For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

        Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Alignment metrics

        This module parses the output from samtools stats. All numbers in millions.

        loading..

        Samtools Flagstat

        This module parses the output from samtools flagstat. All numbers in millions.

        loading..

        Mapped reads per contig

        The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Salmon

        Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        STAR

        STAR is an ultrafast universal RNA-seq aligner.

        Alignment Scores

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        fastp

        fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)

        Filtered Reads

        Filtering statistics of sampled reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Duplication Rates

        Duplication rates of sampled reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Insert Sizes

        Insert size estimation of sampled reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality

        Average sequencing quality over each base of all reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        GC Content

        Average GC content over each base of all reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        N content

        Average N content over each base of all reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).